A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs and its application to the detection of alternative splicing in RNA-seq data

Gustavo Akio Tominaga Sacomoto 1 Vincent Lacroix 1 Marie-France Sagot 1, *
* Corresponding author
1 BAMBOO - An algorithmic view on genomes, cells, and environments
Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
Abstract : We present a new algorithm for enumerating bubbles with length constraints in directed graphs. This problem arises in transcriptomics, where the question is to identify all alternative splicing events present in a sample of mRNAs sequenced by RNA-seq. This is the fi rst polynomial-delay algorithm for this problem and we show that in practice, it is faster than previous approaches. This enables us to deal with larger instances and therefore to discover novel alternative splicing events, especially long ones, that were previously overseen using existing methods.
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https://hal.inria.fr/hal-00842982
Contributor : Marie-France Sagot <>
Submitted on : Wednesday, July 10, 2013 - 7:05:20 AM
Last modification on : Saturday, September 28, 2019 - 1:12:45 AM

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Gustavo Akio Tominaga Sacomoto, Vincent Lacroix, Marie-France Sagot. A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs and its application to the detection of alternative splicing in RNA-seq data. Workshop on Algorithms in Bioinformatics (WABI), Sep 2013, Nice, France. ⟨hal-00842982⟩

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